Contacts of the strand formed by residues 303 - 314 (chain A) in PDB entry 4LEY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ASN* 3.6 18.9 - - - +
297A LEU* 4.9 13.6 - - + +
298A ILE 3.4 7.0 - - - +
299A ARG* 4.9 24.2 + - + +
301A PRO 5.2 2.2 - - - +
302A GLU* 1.3 75.3 - - - +
304A ILE* 1.3 62.5 + - - +
305A SER 4.3 0.4 + - - -
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA* 3.7 31.0 - - + +
170A THR* 5.3 0.4 - - - -
171A VAL* 3.9 10.5 - - + -
209A PRO 4.1 8.7 - - - +
210A ASN* 3.7 6.5 - - - +
212A PHE* 3.5 34.5 - - + -
296A LEU 3.6 1.4 - - - +
297A LEU* 3.8 1.9 - - - -
298A ILE* 2.9 45.1 + - + +
300A ASN* 3.7 28.7 - - + -
302A GLU* 3.9 16.2 - - + +
303A GLU* 1.3 78.7 - - - +
305A SER* 1.3 66.3 + - - +
306A VAL* 4.2 2.9 + - + -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASN 2.7 16.9 + - - -
211A GLU* 3.4 13.6 + - - +
212A PHE* 2.9 24.9 + - - +
295A THR* 3.4 20.9 - - - +
296A LEU 3.5 4.9 - - - -
297A LEU* 5.1 4.3 - - - +
304A ILE* 1.3 75.2 - - - +
306A VAL* 1.3 64.5 + - - +
307A ASP* 3.7 6.9 + - - -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.1 18.4 - - + -
174A VAL* 6.3 0.9 - - + -
175A VAL* 4.3 9.9 - - + -
212A PHE* 3.4 15.0 - - + +
214A VAL* 4.3 11.0 - - + -
294A VAL 3.5 1.0 - - - +
295A THR* 3.3 2.6 - - - -
296A LEU* 2.9 47.3 + - + +
298A ILE* 3.8 30.3 - - + -
304A ILE* 4.4 2.0 - - + -
305A SER* 1.3 79.8 + - - +
307A ASP* 1.3 63.7 + - - +
308A ILE* 3.5 25.8 + - + -
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLU* 5.5 4.4 - - - +
212A PHE 2.9 11.6 + - - +
213A ASP* 4.2 17.7 - - - +
214A VAL* 2.9 29.8 + - - +
291A SER* 5.5 0.9 + - - -
293A ALA* 3.9 16.2 - - + +
294A VAL 4.0 2.7 - - - -
295A THR* 3.3 29.0 + - - +
305A SER* 3.7 7.3 + - - -
306A VAL* 1.3 69.7 - - - +
308A ILE* 1.3 62.2 + - - +
309A ILE* 3.5 9.1 + - + +
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 4.3 12.3 - - + -
178A LEU* 4.3 15.0 - - + -
214A VAL* 3.5 18.4 - - + -
216A PHE* 3.9 29.2 - - + -
266A PHE* 3.8 30.5 - - + -
270A ILE* 4.0 11.0 - - + -
293A ALA* 3.3 2.9 - - - -
294A VAL 2.9 38.6 + - - +
296A LEU* 4.2 17.3 - - + -
306A VAL* 3.9 19.1 - - + +
307A ASP* 1.3 69.6 - - - +
309A ILE* 1.3 60.5 + - - +
310A LEU 3.6 1.7 + - - -
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A THR* 4.4 4.7 - - - +
213A ASP* 4.3 27.8 - - + +
214A VAL 2.9 17.1 + - - +
215A MET* 3.5 26.1 - - + +
216A PHE 2.9 28.2 + - - -
266A PHE* 4.8 1.1 - - - -
292A PRO* 3.8 22.2 - - + +
293A ALA* 3.9 14.6 - - + -
307A ASP* 4.0 7.6 - - + +
308A ILE* 1.3 70.3 - - - +
310A LEU* 1.3 64.7 + - - +
311A ALA 3.6 0.5 + - - -
348A VAL* 3.6 30.1 - - + -
368A SER* 5.8 1.6 - - - +
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 3.8 23.8 - - + -
192A VAL* 5.6 2.2 - - + -
216A PHE 3.8 7.6 - - - +
218A LEU* 5.7 1.6 - - + -
262A MET* 4.0 35.9 - - + +
263A LEU* 4.0 29.2 - - + +
266A PHE* 3.9 31.2 - - + -
292A PRO 3.4 12.6 + - - +
308A ILE 3.6 3.6 + - - -
309A ILE* 1.3 70.5 - - - +
311A ALA* 1.3 70.6 + - - +
312A LEU* 5.9 0.4 - - + -
348A VAL* 3.7 7.6 - - - +
349A PRO* 3.4 29.9 - - + +
363A TRP* 5.1 4.0 - - + -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A MET* 4.5 13.5 - - + -
216A PHE 2.9 14.7 + - - +
217A LYS* 3.4 14.4 - - + -
218A LEU* 2.9 28.4 + - - +
309A ILE 4.5 3.1 - - - +
310A LEU* 1.3 79.4 - - - +
312A LEU* 1.3 65.8 - - - +
346A TYR* 4.4 14.6 - - + -
347A LEU 3.2 9.4 - - - +
348A VAL* 4.5 9.2 - - + -
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 3.3 6.5 - - + +
220A VAL* 3.7 28.3 - - + -
223A ILE* 5.2 2.2 - - + -
237A VAL* 4.3 15.7 - - + -
257A LEU* 3.8 14.4 - - + -
262A MET* 3.7 26.9 - - + -
310A LEU* 5.8 1.3 - - + -
311A ALA* 1.3 77.9 - - - +
313A GLU* 1.3 61.1 + - - +
314A SER 3.9 0.3 + - - -
345A PHE 3.7 0.7 - - - +
346A TYR* 3.3 8.0 - - - -
347A LEU* 2.9 45.4 + - + +
363A TRP* 3.7 43.5 - - + -
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLU* 4.7 1.4 - - - +
217A LYS* 2.7 30.9 + - + +
218A LEU 2.9 11.0 + - - +
219A GLU* 3.3 24.7 - - + +
220A VAL* 3.2 24.1 + - - +
311A ALA 4.1 0.8 - - - -
312A LEU* 1.3 72.6 - - - +
314A SER* 1.3 64.0 + - - +
315A LYS* 3.6 25.8 - - + -
344A PRO* 3.5 25.5 - - + +
345A PHE 3.8 3.4 - - - -
346A TYR* 2.7 35.6 + - + -
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLU* 5.5 0.2 - - - -
220A VAL 4.7 3.8 + - - -
221A PRO 5.1 0.9 + - - -
223A ILE* 3.8 29.8 - - - +
312A LEU 3.9 0.8 + - - -
313A GLU* 1.3 74.4 - - - +
315A LYS* 1.3 62.1 + - - +
316A GLY* 3.8 6.1 + - - -
344A PRO* 3.1 5.8 - - - +
345A PHE* 2.9 71.6 + - - -
347A LEU* 5.6 2.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il